3VPN | pdb_00003vpn

Crystal structure of human ribonucleotide reductase subunit M2 (hRRM2) mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OLJ	PDB ENTRY 3OLJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	50mM Tris-HCl, 0.1mM KCl, pH 7.5, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.91	68.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.082	α = 90
b = 109.082	β = 90
c = 176.523	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2011-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9795	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	50	99.9	0.074	10.5	9.6	51206	51165	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	100		0.692		9.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3OLJ	2.25	35.34	51136	48252	2577	99.4	0.21335	0.21162	0.21	0.24671	0.24	RANDOM	45.436

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.11			1.11		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.986
r_dihedral_angle_4_deg	15.534
r_dihedral_angle_3_deg	14.41
r_dihedral_angle_1_deg	4.755
r_scangle_it	3.226
r_scbond_it	1.951
r_mcangle_it	1.31
r_angle_refined_deg	1.137
r_mcbond_it	0.671
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4732
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling